Results 11 to 20 of about 576,865 (218)

The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection

Genome Biology, 2023
Background The mutational landscape of SARS-CoV-2 varies at the dominant viral genome sequence and minor genomic variant population. During the COVID-19 pandemic, an early substitution in the genome was the D614G change in the spike protein, associated ...
Hannah Goldswain, Xiaofeng Dong, Rebekah Penrice-Randal, Muhannad Alruwaili, Ghada T. Shawli, Tessa Prince, Maia Kavanagh Williamson, Jayna Raghwani, Nadine Randle, Benjamin Jones, I’ah Donovan-Banfield, Francisco J. Salguero, Julia A. Tree, Yper Hall, Catherine Hartley, Maximilian Erdmann, James Bazire, Tuksin Jearanaiwitayakul, Malcolm G. Semple, Peter J. M. Openshaw, J. Kenneth Baillie, ISARIC4C Investigators, Stevan R. Emmett, Paul Digard, David A. Matthews, Lance Turtle, Alistair C. Darby, Andrew D. Davidson, Miles W. Carroll, Julian A. Hiscox   +29 more
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Viral metagenomics updated the prevalence of human papillomavirus types in anogenital warts

Emerging Microbes and Infections, 2019
To investigate the composition of human papillomavirus (HPV) types in anogenital warts (AGWs), viral nucleic acid in 110 AGWs, pooled into 11 specimen pools, were subjected to viral metagenomic analysis.
Hui Xu, Yu Ling, Yuan Xi, Hong Ma, Hao Wang, Hui-Min Hu, Qi Liu, Yu-Mei Li, Xu-Tao Deng, Shi-Xing Yang, Eric Delwart, Wen Zhang   +11 more
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HCMV Envelope Glycoprotein Diversity Demystified

Frontiers in Microbiology, 2019
Human cytomegalovirus (HCMV) is the leading viral cause of congenital birth defects and is responsible for morbidity and mortality in immunosuppressed individuals.
Mathilde Foglierini, Mathilde Foglierini, Jessica Marcandalli, Laurent Perez   +3 more
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Analysis of viral diversity for vaccine target discovery

BMC Medical Genomics, 2017
Background Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and ...
Asif M. Khan, Yongli Hu, Olivo Miotto, Natascha M. Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan, J. Thomas August   +8 more
doaj   +1 more source

An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology

Viruses, 2022
The use of viral sequence data to inform public health intervention has become increasingly common in the realm of epidemiology. Such methods typically utilize multiple sequence alignments and phylogenies estimated from the sequence data.
Colin Young, Sarah Meng, Niema Moshiri
doaj   +1 more source

SARS transmission pattern in Singapore reassessed by viral sequence variation analysis.

PLoS Medicine, 2005
BackgroundEpidemiological investigations of infectious disease are mainly dependent on indirect contact information and only occasionally assisted by characterization of pathogen sequence variation from clinical isolates.
Jianjun Liu, Siew Lan Lim, Yijun Ruan, Ai Ee Ling, Lisa F P Ng, Christian Drosten, Edison T Liu, Lawrence W Stanton, Martin L Hibberd   +8 more
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MRKAd5 HIV-1 Gag/Pol/Nef vaccine-induced T-cell responses inadequately predict distance of breakthrough HIV-1 sequences to the vaccine or viral load. [PDF]

PLoS ONE, 2012
The sieve analysis for the Step trial found evidence that breakthrough HIV-1 sequences for MRKAd5/HIV-1 Gag/Pol/Nef vaccine recipients were more divergent from the vaccine insert than placebo sequences in regions with predicted epitopes.
Holly Janes, Nicole Frahm, Allan DeCamp, Morgane Rolland, Erin Gabriel, Julian Wolfson, Tomer Hertz, Esper Kallas, Paul Goepfert, David P Friedrich, Lawrence Corey, James I Mullins, M Juliana McElrath, Peter Gilbert   +13 more
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Rapid screening and identification of viral pathogens in metagenomic data

BMC Medical Genomics, 2021
Background Virus screening and viral genome reconstruction are urgent and crucial for the rapid identification of viral pathogens, i.e., tracing the source and understanding the pathogenesis when a viral outbreak occurs.
Shiyang Song, Liangxiao Ma, Xintian Xu, Han Shi, Xuan Li, Yuanhua Liu, Pei Hao   +6 more
doaj   +1 more source

Viral escape mutations do not account for non-protection from SIVmac239 challenge in RhCMV/SIV vaccinated rhesus macaques

Frontiers in Immunology
Simian immunodeficiency virus (SIV) vaccines based upon 68-1 Rhesus Cytomegalovirus (RhCMV) vectors show remarkable protection against pathogenic SIVmac239 challenge.
Benjamin N. Bimber, Benjamin N. Bimber, Justine Sunshine, G. W. McElfresh, Jason S. Reed, Reese Pathak, Katherine B. Bateman, Colette M. Hughes, Roxanne M. Gilbride, Julia C. Ford, David Morrow, Jeffrey D. Lifson, Jonah B. Sacha, Jonah B. Sacha, Scott G. Hansen, Scott G. Hansen, Louis J. Picker, Louis J. Picker   +17 more
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Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation [PDF]

PeerJ
Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting ...
Haoqiu Song, Saima Sultana Tithi, Connor Brown, Frank O. Aylward, Roderick Jensen, Liqing Zhang   +5 more
doaj   +2 more sources